S Roepcke

Summary

Affiliation: Max Planck Institute for Molecular Genetics
Country: Germany

Publications

  1. ncbi Comparative promoter region analysis powered by CORG
    Christoph Dieterich
    Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    BMC Genomics 6:24. 2005
  2. ncbi Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters
    Stefan Roepcke
    Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany
    Gene 365:48-56. 2006
  3. ncbi T-Reg Comparator: an analysis tool for the comparison of position weight matrices
    Stefan Roepcke
    Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    Nucleic Acids Res 33:W438-41. 2005
  4. ncbi SVC: structured visualization of evolutionary sequence conservation
    S Roepcke
    Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    Nucleic Acids Res 33:W271-3. 2005
  5. ncbi Inferring differentiation pathways from gene expression
    Ivan G Costa
    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
    Bioinformatics 24:i156-64. 2008
  6. ncbi Alternative polyadenylation signals and promoters act in concert to control tissue-specific expression of the Opitz Syndrome gene MID1
    Jennifer Winter
    Max Planck Institute for Molecular Genetics, Berlin Dahlem, Germany
    BMC Mol Biol 8:105. 2007
  7. ncbi Gene expression trees in lymphoid development
    Ivan G Costa
    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
    BMC Immunol 8:25. 2007
  8. ncbi Comparative 3'UTR analysis allows identification of regulatory clusters that drive Eph/ephrin expression in cancer cell lines
    Jennifer Winter
    Max Planck Institute for Molecular Genetics, Berlin Dahlem, Germany
    PLoS ONE 3:e2780. 2008
  9. ncbi An expression module of WIPF1-coexpressed genes identifies patients with favorable prognosis in three tumor types
    Eike Staub
    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
    J Mol Med (Berl) 87:633-44. 2009
  10. ncbi MACAT--microarray chromosome analysis tool
    Joern Toedling
    Freie Universitaet Berlin, Bioinformatics programme and Max Planck Institute for Molecular Genetics, Germany
    Bioinformatics 21:2112-3. 2005

Collaborators

Detail Information

Publications13

  1. ncbi Comparative promoter region analysis powered by CORG
    Christoph Dieterich
    Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    BMC Genomics 6:24. 2005
    ..To support promoter analysis, we present CORG http://corg.molgen.mpg.de, a framework for studying upstream regions including untranslated exons (5' UTR)...
  2. ncbi Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters
    Stefan Roepcke
    Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany
    Gene 365:48-56. 2006
    ..Such a factor binds the target DNA at a fixed location relative to the TSS, and possibly interacts directly with the basal transcription machinery...
  3. ncbi T-Reg Comparator: an analysis tool for the comparison of position weight matrices
    Stefan Roepcke
    Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    Nucleic Acids Res 33:W438-41. 2005
    ..Typical areas of application for T-Reg Comparator are motif and regulatory module finding and annotation of regulatory genomic regions. T-Reg Comparator is available at http://treg.molgen.mpg.de...
  4. ncbi SVC: structured visualization of evolutionary sequence conservation
    S Roepcke
    Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    Nucleic Acids Res 33:W271-3. 2005
    ..A particular application of our tool arises from the fact that around mRNA editing sites both exonic and intronic sequences are highly conserved. This aids in delineation of these sites. SVC is available at http://svc.molgen.mpg.de...
  5. ncbi Inferring differentiation pathways from gene expression
    Ivan G Costa
    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
    Bioinformatics 24:i156-64. 2008
    ..In general, the similarities in the gene expression programs of cell populations reflect the similarities in the differentiation path...
  6. ncbi Alternative polyadenylation signals and promoters act in concert to control tissue-specific expression of the Opitz Syndrome gene MID1
    Jennifer Winter
    Max Planck Institute for Molecular Genetics, Berlin Dahlem, Germany
    BMC Mol Biol 8:105. 2007
    ..Previous Northern blot analyses revealed the existence of at least three MID1 transcripts of differing lengths...
  7. ncbi Gene expression trees in lymphoid development
    Ivan G Costa
    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
    BMC Immunol 8:25. 2007
    ....
  8. ncbi Comparative 3'UTR analysis allows identification of regulatory clusters that drive Eph/ephrin expression in cancer cell lines
    Jennifer Winter
    Max Planck Institute for Molecular Genetics, Berlin Dahlem, Germany
    PLoS ONE 3:e2780. 2008
    ..Together our studies suggest that overexpression of HuR as found in many progressive tumors could be causative for disarranged Eph receptor to ephrin ligand ratios leading to a higher degree of tissue invasiveness...
  9. ncbi An expression module of WIPF1-coexpressed genes identifies patients with favorable prognosis in three tumor types
    Eike Staub
    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
    J Mol Med (Berl) 87:633-44. 2009
    ....
  10. ncbi MACAT--microarray chromosome analysis tool
    Joern Toedling
    Freie Universitaet Berlin, Bioinformatics programme and Max Planck Institute for Molecular Genetics, Germany
    Bioinformatics 21:2112-3. 2005
    ..AVAILABILITY: The R-package MACAT can be obtained from http://www.compdiag.molgen.mpg.de/software/macat.shtml SUPPLEMENTARY INFORMATION: http://www.compdiag.molgen.mpg.de/software/macat.shtml...
  11. ncbi WIF1, a component of the Wnt pathway, is down-regulated in prostate, breast, lung, and bladder cancer
    Christoph Wissmann
    metaGen Pharmaceuticals GmbH, Oudenarder Strasse 16, 13347 Berlin, Germany
    J Pathol 201:204-12. 2003
    ..However, down-regulation of WIF1 correlated with higher tumour stage in urinary bladder tumours (pTa versus pT1-pT4; p = 0.038)...
  12. ncbi Transcriptional census of 36 microdissected colorectal cancers yields a gene signature to distinguish UICC II and III
    Joern Groene
    Department of General, Vascular and Thoracic Surgery, Campus Benjamin Franklin, Charite Universitaetsmedizin, Berlin, Germany
    Int J Cancer 119:1829-36. 2006
    ....
  13. ncbi Expression profiling of microdissected matched prostate cancer samples reveals CD166/MEMD and CD24 as new prognostic markers for patient survival
    Glen Kristiansen
    Institute of Pathology, Charite University Hospital, Berlin, Germany
    J Pathol 205:359-76. 2005
    ..7, p = 0.006) in a Cox regression model, and was also superior to conventional markers. This combination of molecular markers thus appears to allow improved prediction of patient prognosis, but should be validated in larger studies...